Research workbench
Crystal structure of deoxygenated hemoglobin in complex with sphingosine phosphate
Analyse Crystal structure of deoxygenated hemoglobin in complex with sphingosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KSJ
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, S1P
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 76% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- S1P · (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.79 | 0.83 | 67 | S1P |
| 2 | 229 | 0.75 | 0.88 | 31 | HEM |
| 3 | 232 | 0.74 | 0.87 | 30 | HEM |
| 4 | 272 | 0.72 | 0.85 | 30 | HEM |
| 5 | 289 | 0.71 | 0.84 | 35 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 863 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 851 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 715 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 714 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5KSJ · Crystal structure of deoxygenated hemoglobin in complex with Sphingosine phosphate · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 5KSJ · PDBe 5KSJ · UniProt P69905 · UniProt P68871
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